Auditor-General Kimi Makwetu has made a grim assessment of the state of the department's finances, warning that they cast "significant doubt" on its ability to continue as a going concern.

The department's annual report reflects a continuing inability to curb unauthorised and irregular, fruitless and wasteful expenditure and a failure to act against the officials responsible.

Makwetu based his qualified opinion on the department's R119 million overdraft and cumulative unauthorised spending of R933 million and an amount of just over R2 billion owing to creditors.

Citing a lack of internal controls, Makwetu says he couldn't determine the figures for irregular, fruitless and wasteful spending by the department and believes they're understated.

He has also red-flagged the department's water trading entity, which racked up fruitless and wasteful expenditure of more than R1 billion and irregular expenditure of nearly R5 billion. It is sitting with an overdraft of R1.4 billion, a slight improvement on last year's R2.1 billion.